pross

Overview

Pross is a python module including functions for the analysis of PDB files. It includes utilities for calculating torsion angles, as well as methods for assigning secondary structures and mesostate codes. Originally Written by Pat Fleming, the Pross module was intended to reproduce functionality of the BIOMOL collection without the need to install the entire BIOMOL distribution.

Download

pross.py v463, July 9th, 2010

Support

hpc-devel@sbgrid.org

Examples

Below is an example of using the pross module to separate secondary structures from groups of residues:

:::python
import os.path
import pross as p 

def trimfile(in_fp, out_fp):
    if not os.path.exists(in_fp):
        return

    pdb = p.PDBFile(in_fp)
    chains = pdb.read(as_protein=1)

    for chain in chains.elements:
        (a, b, c, sst_list) = p.rc_ss(chain)

        idx = 0
        for res_class in sst_list:
            if res_class not in ["H", "E"]:
               chain.elements[idx] = []
            idx += 1


    mol = p.molMol(chains=chains)
    p.write_pdb(mol, out_fp) # write modified PDB to disk

This function reads a pdb file and iterates through each of the residues and removes residues that are not in the 'H' (Helix) or 'E' (Strand) residue classes.

Documentation

PROSS Module API

Usage

pross.py pdbfile [oldmeso | fgmeso]

Choose old mesostate definitions or finegrained mesostate definitions. Default is finegrained.

Imported Modules

Pross utilizes the following modules:

• sys
• string
• re
• copy
• gizp
• math
• types

Data Structures

TypedList

A Python list restricted to having objects of the same type. An instance of a TypedList is created as follows:

mylist = TypedList(function, [elements])

where function is a python function which takes an argument and returns 1 or 0 indicating whether the object represented by the argument is of the correct type, and elements is an optional list of elements to be added into the instance. Here is a full blown example.

:::python
def is_int(o):

    return type(o) == type(0)

mylist = TypedList(is_int, [0, 1, 2, 3])

New elements are added to the list as follows: mylist.append(25)

Instances of TypedList support all operations available for Python Lists (as of Python version 1.5.2a2)

Major Functions

• res_rc

  res_rc(r1, r2, r3) - Get mesostate code for a residue

  Given a phi (r1), psi (r2), and omega (r3) torsion angle, calculate the mesostate code that describes that residue. A mesostate will be returned in all but two cases: if omega deviates from planarity by more than 90 degrees, '*' is returned. Also, if any torsions are greater than 180.0 (biomol assignes 999.0 degrees to angles that that are indeterminate), prosst.INVALID is returned. Here, r3 defaults to 180.0.

• rc_codes

  rc_codes(chain, phi, psi, ome) - return rotamer codes

  Given a protein chain (and optionally phi, psi, omega), this function will return a list of mesostate codes that applies to the chain, as determined by res_rc.

• rc_ss

  rc_ss(chain, phi, psi, ome) - calculate secondary structure

  This function calculates the secondary structure using the PROSS method with rotamer codes. Given a chain, and optionally a list of phi, psi, and omega, it calculates the backbone secondary structure of the chain. The return value is (phi, psi, ome, sst), where phi, psi, and ome are calculated if not specified, and sst is the secondary structure codes: H = helix, E = strand, P = PII, C = coil.

• _rc_find

  _rc_find(codes, pat_obj) - find a endpoints of a regexp

  Given a list of mesostate codes, this function identifies a endpoints of a match . <pat_obj> is a compiled regular expression pattern whose matches will be returned as pairs indicated start, end in

• write_pdb

  write_pdb - write a PDB file from a molecular object

  write_pdb takes a biomol.Mol object and creates a PDB file based on the definitions given. It can support all atomic properties as well as insertion codes and alternate locations. Essentially, biomol is designed such that if the original molecule has all that stuff it will be retained in the final PDB file. If that is not desired, you must make the modifications to the Mol object yourself (or use one of the utilities).

  write_pdb takes the following arguments:

  • myMol -- The mol.Mol object to be written.

  • f -- A file instruction. This can be a string, in which case f will be interpreted as a filename. If the string f ends with .gz, the resulting file will be compressed using gzip. Alternatively, f can be an open file object (it must have the write attribute). If f is an object, the PDB will be written to the object. When f is a file object, SEQRES and END records will not be written by default.

  • seq -- A boolean that determines whether SEQRES records will be written. By default this is true (except in the case where f is an object).